extremely fast Smith-waterman aligments

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ryan_m
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extremely fast Smith-waterman aligments

A few companies have released specialised hardware for performing common bioinformatics operations, such as the smith-waterman dyamic programming alignment algorithm.
DeCypher is one of them. It looks like they are running this algorithm 500 times faster with the help of their hardware. I wonder if something can be done to speed up BLAST in the same way (since it uses a DP algorithm to construct its alignments). I guess the payoff would depend on how much of its time is spent on aligning vs on searching. If hardware is released, I'd like to see NCBI purchase it, so we don't have to sit around tapping our fingers so much while we wait for our BLAST results!

Chris Hoover
Chris Hoover's picture
ryan_m wrote:A few companies

ryan_m wrote:

A few companies have released specialised hardware for performing common bioinformatics operations, such as the smith-waterman dyamic programming alignment algorithm.
DeCypher is one of them. It looks like they are running this algorithm 500 times faster with the help of their hardware. I wonder if something can be done to speed up BLAST in the same way (since it uses a DP algorithm to construct its alignments). I guess the payoff would depend on how much of its time is spent on aligning vs on searching. If hardware is released, I'd like to see NCBI purchase it, so we don't have to sit around tapping our fingers so much while we wait for our BLAST results!

Ryan

I'm with the TimeLogic team at Active Motif, and wanted to let you know that we also accelerate other commonly used bioinformatics applications. Tera-BLAST is our accelerated BLAST application. Our implementation is something of a fusion of ideas from NCBI and Wu-BLAST. Tera-Probe is an extension to Tera-BLAST that offers Smith-Waterman sensitivity for oligo searches, but at accelerated BLAST speeds.

Take a look at our algorithms page to see the complete scope of applications that are available on our DeCypher and CodeQuest biocomputing systems. If you have questions on the systems, please contact us to schedule a free performance benchmark.